breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJBEI_Xylose_A27_F39_I1_S23_R1_001.good.fq1,006,223133,912,928100.0%133.1 bases136 bases96.9%
errorsJBEI_Xylose_A27_F39_I1_S23_R2_001.good.fq1,006,223133,912,928100.0%133.1 bases136 bases82.8%
total2,012,446267,825,856100.0%133.1 bases136 bases89.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,183,85843.98.4100.0%na
total6,183,858100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 1000003716
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000147
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.90328

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input20:47:09 17 Jul 202020:48:04 17 Jul 202055 seconds
Read alignment to reference genome20:48:05 17 Jul 202020:52:41 17 Jul 20204 minutes 36 seconds
Preprocessing alignments for candidate junction identification20:52:41 17 Jul 202020:53:30 17 Jul 202049 seconds
Preliminary analysis of coverage distribution20:53:30 17 Jul 202020:54:34 17 Jul 20201 minute 4 seconds
Identifying junction candidates20:54:34 17 Jul 202020:54:35 17 Jul 20201 second
Re-alignment to junction candidates20:54:35 17 Jul 202020:55:43 17 Jul 20201 minute 8 seconds
Resolving best read alignments20:55:43 17 Jul 202020:57:16 17 Jul 20201 minute 33 seconds
Creating BAM files20:57:16 17 Jul 202020:58:06 17 Jul 202050 seconds
Tabulating error counts20:58:06 17 Jul 202020:58:42 17 Jul 202036 seconds
Re-calibrating base error rates20:58:42 17 Jul 202020:58:45 17 Jul 20203 seconds
Examining read alignment evidence20:58:45 17 Jul 202021:04:51 17 Jul 20206 minutes 6 seconds
Polymorphism statistics21:04:51 17 Jul 202021:04:52 17 Jul 20201 second
Output21:04:52 17 Jul 202021:06:10 17 Jul 20201 minute 18 seconds
Total 19 minutes 0 seconds